Courses

BIOHOPK 183H

BIOHOPK 183H

The course is designed to provide background on key concepts in ecology, familiarize students with key ecological processes and ecosystems, and the methods used in ecological studies. The course will further build students¿ skills in critical scientific thinking, reading the literature, and scientific communication. A major goal of the course is to train students to ask questions in ecology, and to design, conduct and report studies addressing these questions. Thus, emphasis is also placed, in additional to general ecological concepts, on field observations, experimental design, and the analysis, interpretation and presentation of ecological data (through computer laboratories, written assignments and presentations). Written assignments, presentations and discussions are designed to provide experience in organizing and presenting information and to expose students to multiple perspectives on ecological processes and their applications.nThis course fulfills the same requirement as BIO 81.

Course Quarter: Autumn

BIO 3

BIO 3

An introduction to contemporary research in marine biology, including ecology, conservation biology, environmental toxicology, behavior, biomechanics, evolution, neurobiology, and molecular biology. Emphasis is on new discoveries and the technologies used to make them. Weekly lectures by faculty from the Hopkins Marine Station.

BIO 12N

BIO 12N

Animals living in the oceans experience a highly varied range of environmental stimuli. An aquatic lifestyle requires an equally rich range of sensory adaptations, including some that are totally foreign to us. In this course we will examine sensory system in marine animals from both an environmental and behavioral perspective and from the point of view of neuroscience and information systems engineering.

BIOHOPK 198H

BIOHOPK 198H

May be taken as a prelude to research and may also involve participation in a lab or research group seminar and/or library research. Credit for work arranged with out-of-department instructors restricted to Biology majors and requires department approval. May be repeated for credit. (Staff)

BIOHOPK 315H

BIOHOPK 315H

The course will cover multiple skills required to succeed in graduate school and beyond, including fund raising, publishing, selecting career options, job application and negotiation, and teaching, through lectures, group discussions, and practical excercises.

Course Quarter: Winter

BIO 3N

BIO 3N

The state of a changing world ocean, particularly in the eastern Pacific, will be examined through historical and contemporary fiction, non-fiction and scientific publications. Issues will include harvest and mariculture fisheries, land-sea interactions and oceanic climate change in both surface and deep waters.

BIOHOPK 140H

BIOHOPK 140H

(Graduate students register for 240H.) Introduction to applied statistical modeling in a Bayesian framework. Topics will include probability, regression, model comparison, and hierarchical modeling. We will take a hands-on, computational approach (R, Stan) to gain intuition so that students can later design their own inferential models. Prerequisites for this course include introductory statistics and some calculus or linear algebra, as well as previous exposure to scientific computing. Open to graduate students; undergraduate students may enroll with consent of instructor.

BIOHOPK 157H

BIOHOPK 157H

What role does creativity play in the life of a scientist? How has science inspired great literature? How do you write accessibly and expressively about things like whales, DNA or cancer? This course begins with a field trip to Hopkins Marine Station, perched at the edge of the Pacific, where Stanford labs buzz with activity alongside barking seals and crashing waves. Here, in this spectacular setting, we learn to pay attention to our encounters with the natural world and translate sensory experience to the page. Students keep field journals to collect observations and cultivate a reflective practice. In-class writing experiments lead to original nonfiction combining personal narrative and scientific curiosity. Students workshop their projects, receiving supportive feedback from the group. You will develop a more patient and observant eye, improve your ability to articulate scientific concepts, and, hopefully, have a bit of fun along the way.nNOTE: First priority to undergrads. Students must attend the first class meeting to retain their roster spot.

BIOHOPK 198H

BIOHOPK 198H

May be taken as a prelude to research and may also involve participation in a lab or research group seminar and/or library research. Credit for work arranged with out-of-department instructors restricted to Biology majors and requires department approval. May be repeated for credit. (Staff)

BIOHOPK 240H

BIOHOPK 240H

(Graduate students register for 240H.) Introduction to applied statistical modeling in a Bayesian framework. Topics will include probability, regression, model comparison, and hierarchical modeling. We will take a hands-on, computational approach (R, Stan) to gain intuition so that students can later design their own inferential models. Prerequisites for this course include introductory statistics and some calculus or linear algebra, as well as previous exposure to scientific computing. Open to graduate students; undergraduate students may enroll with consent of instructor.

BIOHOPK 257H

BIOHOPK 257H

What role does creativity play in the life of a scientist? How has science inspired great literature? How do you write accessibly and expressively about things like whales, DNA or cancer? This course begins with a field trip to Hopkins Marine Station, perched at the edge of the Pacific, where Stanford labs buzz with activity alongside barking seals and crashing waves. Here, in this spectacular setting, we learn to pay attention to our encounters with the natural world and translate sensory experience to the page. Students keep field journals to collect observations and cultivate a reflective practice. In-class writing experiments lead to original nonfiction combining personal narrative and scientific curiosity. Students workshop their projects, receiving supportive feedback from the group. You will develop a more patient and observant eye, improve your ability to articulate scientific concepts, and, hopefully, have a bit of fun along the way.nNOTE: First priority to undergrads. Students must attend the first class meeting to retain their roster spot.

BIOHOPK 299H

BIOHOPK 299H

Graduate students only. Topics will change from year to year but will include such topics as sustainable fisheries, protected areas, ocean planning, social-ecological systems, dynamic management, sustainable seafood, and impacts of climate change

BIOHOPK 330H

BIOHOPK 330H

This writer's seminar will workshop the elements of good scientific writing by focusing on a paper's Introduction. We will chart the elements of an effective Introduction, designed for different audiences and types of scientific journals. The course will provide participants with the chance to craft an Introduction to a current paper or proposal and have it evaluated in light of the ideal structure we define.

Course Quarter: Spring

BIO 140

BIO 140

Covers the way marine animals and plants live in extreme environments by examining morphological, ecological, and genetic adaptations to low temperature, high heat, deep water, etc. We also cover extreme lifestyles such as fast swimming, small and large body size, and novel reproductive systems. Lecture material is punctuated with a series of tutorials on narrative writing skills in science, especially creative non-fiction, memoirs, braided essays and short fiction. The goal is to integrate quantitative thinking about the life sciences with creative writing that brings facts to life. Prerequisites: core courses in biology, creative writing, environmental sciences or engineering. Two lectures back to back on Tuesdays with a Writing Intermezzo between.

BIOHOPK 47

BIOHOPK 47

This course is a field-based inquiry into rocky intertidal shores that introducesnstudents to ecology and environmental physiology and the research methods used to study them. Students will learn how to detect patterns quantitatively in nature through appropriate sampling methods & statistical analysis. Following exploration of appropriate background material in class and through exploration of the scientific literature, students will learn how to formulate testable hypotheses regarding the underlying causes of the patterns they discern. A variety of different aspects of ecology and physiology will be investigated cooperatively by the students during the quarter, culminating in development of an individual final paper in the form of a research proposal based on data collected during the course. The course will provide a broad conceptual introduction to the underlying biological principles that influence adaptation to the planet¿s dynamic habitats, as well as inquiry-based experience in how to explore and understand complex systems in nature. nThis course fulfills the same laboratory requirement as BIO 47. Satisfies WIM in Biology.

BIOHOPK 81

BIOHOPK 81

The course is designed to provide background on key concepts in ecology, familiarize students with key ecological processes and ecosystems, and the methods used in ecological studies. The course will further build students¿ skills in critical scientific thinking, reading the literature, and scientific communication. A major goal of the course is to train students to ask questions in ecology, and to design, conduct and report studies addressing these questions. Thus, emphasis is also placed, in additional to general ecological concepts, on field observations, experimental design, and the analysis, interpretation and presentation of ecological data (through computer laboratories, written assignments and presentations). Written assignments, presentations and discussions are designed to provide experience in organizing and presenting information and to expose students to multiple perspectives on ecological processes and their applications.nThis course fulfills the same requirement as BIO 81.

BIOHOPK 150H

BIOHOPK 150H

(Graduate students register for 250H.) The principles of life's physical interactions. We will explore basic physics. fluid mechanics, thermal dynamics, and materials science to see how the principles of these fields can be used to investigate ecology at levels from the individual to the community. Topics include: diffusion, boundary layers, fluid-dynamic forces, locomotion, heat-budget models, fracture mechanics, adhesion, beam theory, the statistics of extremes, and the theory of self-organization. Open to students from all backgrounds. Some familiarity with basic physics and calculus advantageous but not necessary.

BIOHOPK 158H

BIOHOPK 158H

(Graduate students register for 258H.) This course will consider the remarkable nexus of scientific research and literature that developed on the Monterey Peninsula in the first half of the 20th century and how the two areas of creativity influenced each other. The period of focus begins with the 1932 association of John and Carol Steinbeck, Ed Ricketts, and Joseph Campbell, all of whom were highly influenced by the Carmel poet, Robinson Jeffers ¿ and ends with the novels Cannery Row (1945) and Sweet Thursday (1954). An indisputable high-tide mark, Sea of Cortez: A Leisurely of Travel and Research (1941) will be considered in detail. Weekend field trips will include intertidal exploration, a tour of the Jeffers Tor House in Carmel, and whale watching on Monterey Bay.

BIOHOPK 159H

BIOHOPK 159H

Graduate students register for 259H. This course will allow students to learn lab approaches to analyzing DNA to answer questions in parentage, population biology, and species identification. Students will spend 2-3 hours each week in the lab extracting DNA, analyzing sequences, and testing hypotheses. Molecular projects will interface with local research projects and course content.

BIOHOPK 173HA

BIOHOPK 173HA

(Graduate students register for 273HA.). Introduction to the key concepts of ecology and policy relevant to marine conservation issues at the population to ecosystems level. Focus on the origin and maintenance of biodiversity and conservation applications from both the biology and policy perspectives (for example, endangered species, captive breeding, reserve design, habitat fragmentation, ecosystem restoration/rehabilitation). Also includes emerging approaches such as ecosystem based management, ocean planning, and coupled social-ecological systems. The course will include lectures, readings and discussions of primary literature, and attendance at seminars with visiting scholars. Prerequisite: introductory biology; suggested: a policy and/or introductory ecology course.nStudents should enroll in this course if they are only joining the seminar and discussion. Students who will engage in the full course should enroll in BIOHOPK 173H/273H.

BIOHOPK 173H

BIOHOPK 173H

(Graduate students register for 273H.). Introduction to the key concepts of ecology and policy relevant to marine conservation issues at the population to ecosystems level. Focus on the origin and maintenance of biodiversity and conservation applications from both the biology and policy perspectives (for example, endangered species, captive breeding, reserve design, habitat fragmentation, ecosystem restoration/rehabilitation). Also includes emerging approaches such as ecosystem based management, ocean planning, and coupled social-ecological systems. The course will include lectures, readings and discussions of primary literature, and attendance at seminars with visiting scholars. Prerequisite: introductory biology; suggested: a policy and/or introductory ecology course.

BIOHOPK 174H

BIOHOPK 174H

(Graduate students register for 274H.) Variability is an integral part of biology. Introduction to probability and its use in designing experiments to address biological problems. Focus is on experimental design and the use of linear models in testing hypotheses (e.g., analysis of variance, regression). Students will use R to explore and analyze locally relevant biological datasets. No programming or statistical background is assumed. Prerequisite: consent of instructor.

BIOHOPK 182H

BIOHOPK 182H

(Graduate students register for 323H.) Five weeks of marine science including oceanography, marine physiology, policy, maritime studies, conservation, and nautical science at Hopkins Marine Station, followed by five weeks at sea aboard a sailing research vessel in the Pacific Ocean. Shore component comprised of three multidisciplinary courses meeting daily and continuing aboard ship. Students develop an independent research project plan while ashore, and carry out the research at sea. In collaboration with the Sea Education Association of Woods Hole, MA. Only 6 units may count towards the Biology major.

BIOHOPK 198H

BIOHOPK 198H

May be taken as a prelude to research and may also involve participation in a lab or research group seminar and/or library research. Credit for work arranged with out-of-department instructors restricted to Biology majors and requires department approval. May be repeated for credit. (Staff)

BIOHOPK 250H

BIOHOPK 250H

(Graduate students register for 250H.) The principles of life's physical interactions. We will explore basic physics. fluid mechanics, thermal dynamics, and materials science to see how the principles of these fields can be used to investigate ecology at levels from the individual to the community. Topics include: diffusion, boundary layers, fluid-dynamic forces, locomotion, heat-budget models, fracture mechanics, adhesion, beam theory, the statistics of extremes, and the theory of self-organization. Open to students from all backgrounds. Some familiarity with basic physics and calculus advantageous but not necessary.

BIOHOPK 258H

BIOHOPK 258H

(Graduate students register for 258H.) This course will consider the remarkable nexus of scientific research and literature that developed on the Monterey Peninsula in the first half of the 20th century and how the two areas of creativity influenced each other. The period of focus begins with the 1932 association of John and Carol Steinbeck, Ed Ricketts, and Joseph Campbell, all of whom were highly influenced by the Carmel poet, Robinson Jeffers ¿ and ends with the novels Cannery Row (1945) and Sweet Thursday (1954). An indisputable high-tide mark, Sea of Cortez: A Leisurely of Travel and Research (1941) will be considered in detail. Weekend field trips will include intertidal exploration, a tour of the Jeffers Tor House in Carmel, and whale watching on Monterey Bay.

BIOHOPK 259H

BIOHOPK 259H

Graduate students register for 259H. This course will allow students to learn lab approaches to analyzing DNA to answer questions in parentage, population biology, and species identification. Students will spend 2-3 hours each week in the lab extracting DNA, analyzing sequences, and testing hypotheses. Molecular projects will interface with local research projects and course content.

BIOHOPK 273HA

BIOHOPK 273HA

(Graduate students register for 273HA.). Introduction to the key concepts of ecology and policy relevant to marine conservation issues at the population to ecosystems level. Focus on the origin and maintenance of biodiversity and conservation applications from both the biology and policy perspectives (for example, endangered species, captive breeding, reserve design, habitat fragmentation, ecosystem restoration/rehabilitation). Also includes emerging approaches such as ecosystem based management, ocean planning, and coupled social-ecological systems. The course will include lectures, readings and discussions of primary literature, and attendance at seminars with visiting scholars. Prerequisite: introductory biology; suggested: a policy and/or introductory ecology course.nStudents should enroll in this course if they are only joining the seminar and discussion. Students who will engage in the full course should enroll in BIOHOPK 173H/273H.

BIOHOPK 273H

BIOHOPK 273H

(Graduate students register for 273H.). Introduction to the key concepts of ecology and policy relevant to marine conservation issues at the population to ecosystems level. Focus on the origin and maintenance of biodiversity and conservation applications from both the biology and policy perspectives (for example, endangered species, captive breeding, reserve design, habitat fragmentation, ecosystem restoration/rehabilitation). Also includes emerging approaches such as ecosystem based management, ocean planning, and coupled social-ecological systems. The course will include lectures, readings and discussions of primary literature, and attendance at seminars with visiting scholars. Prerequisite: introductory biology; suggested: a policy and/or introductory ecology course.

BIOHOPK 274H

BIOHOPK 274H

(Graduate students register for 274H.) Variability is an integral part of biology. Introduction to probability and its use in designing experiments to address biological problems. Focus is on experimental design and the use of linear models in testing hypotheses (e.g., analysis of variance, regression). Students will use R to explore and analyze locally relevant biological datasets. No programming or statistical background is assumed. Prerequisite: consent of instructor.

BIOHOPK 299H

BIOHOPK 299H

Graduate students only. Topics will change from year to year but will include such topics as sustainable fisheries, protected areas, ocean planning, social-ecological systems, dynamic management, sustainable seafood, and impacts of climate change

BIOHOPK 323H

BIOHOPK 323H

(Graduate students register for 323H.) Five weeks of marine science including oceanography, marine physiology, policy, maritime studies, conservation, and nautical science at Hopkins Marine Station, followed by five weeks at sea aboard a sailing research vessel in the Pacific Ocean. Shore component comprised of three multidisciplinary courses meeting daily and continuing aboard ship. Students develop an independent research project plan while ashore, and carry out the research at sea. In collaboration with the Sea Education Association of Woods Hole, MA. Only 6 units may count towards the Biology major.

Course Quarter: Summer

BIOHOPK 185H

BIOHOPK 185H

(Graduate students register for 285H.) Five week course. Daily lectures, labs, and scuba dives focused on scientific diving and quantitative ecological methods in kelp forests.. Topics include identification and natural history of resident organisms, ecological processes, and subtidal field techniques. Class projects contribute to long-term monitoring at Hopkins Marine Station. It is recommended (but not required) that students complete the Stanford Scientific Diver Training session, typically offered prior to the start of the course. Prerequisites: consent of instructor; rescue scuba certification and scuba equipment.

BIOHOPK 198H

BIOHOPK 198H

May be taken as a prelude to research and may also involve participation in a lab or research group seminar and/or library research. Credit for work arranged with out-of-department instructors restricted to Biology majors and requires department approval. May be repeated for credit. (Staff)

BIOHOPK 285H

BIOHOPK 285H

(Graduate students register for 285H.) Five week course. Daily lectures, labs, and scuba dives focused on scientific diving and quantitative ecological methods in kelp forests.. Topics include identification and natural history of resident organisms, ecological processes, and subtidal field techniques. Class projects contribute to long-term monitoring at Hopkins Marine Station. It is recommended (but not required) that students complete the Stanford Scientific Diver Training session, typically offered prior to the start of the course. Prerequisites: consent of instructor; rescue scuba certification and scuba equipment.